Single-Cell Consensus Clustering

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Documentation for package ‘SC3’ version 1.18.0

Help Pages

ann Cell type annotations for data extracted from a publication by Yan et al.
calculate_distance Calculate a distance matrix
calculate_stability Calculate the stability index of the obtained clusters when changing 'k'
consensus_matrix Calculate consensus matrix
consmx Consensus matrix computation
ED1 Compute Euclidean distance matrix by rows
ED2 Compute Euclidean distance matrix by columns
estkTW Estimate the optimal k for k-means clustering
get_auroc Calculate the area under the ROC curve for a given gene.
get_biolgy Wrapper for calculating biological properties
get_de_genes Find differentially expressed genes
get_marker_genes Calculate marker genes
get_outl_cells Find cell outliers in each cluster.
get_processed_dataset Get processed dataset used by 'SC3' clustering
markers_for_heatmap Reorder and subset gene markers for plotting on a heatmap
norm_laplacian Graph Laplacian calculation
organise_de_genes Get differentiall expressed genes from an object of 'SingleCellExperiment' class
organise_marker_genes Get marker genes from an object of 'SingleCellExperiment' class
prepare_for_svm A helper function for the SVM analysis
reindex_clusters Reindex cluster labels in ascending order
sc3 Run all steps of 'SC3' in one go
sc3-method Run all steps of 'SC3' in one go
sc3.SingleCellExperiment Run all steps of 'SC3' in one go
sc3_calc_biology Calculate DE genes, marker genes and cell outliers.
sc3_calc_biology, Calculate DE genes, marker genes and cell outliers.
sc3_calc_biology-method Calculate DE genes, marker genes and cell outliers.
sc3_calc_biology.SingleCellExperiment Calculate DE genes, marker genes and cell outliers.
sc3_calc_consens Calculate consensus matrix.
sc3_calc_consens, Calculate consensus matrix.
sc3_calc_consens-method Calculate consensus matrix.
sc3_calc_consens.SingleCellExperiment Calculate consensus matrix.
sc3_calc_dists Calculate distances between the cells.
sc3_calc_dists, Calculate distances between the cells.
sc3_calc_dists-method Calculate distances between the cells.
sc3_calc_dists.SingleCellExperiment Calculate distances between the cells.
sc3_calc_transfs Calculate transformations of the distance matrices.
sc3_calc_transfs, Calculate transformations of the distance matrices.
sc3_calc_transfs-method Calculate transformations of the distance matrices.
sc3_calc_transfs.SingleCellExperiment Calculate transformations of the distance matrices.
sc3_estimate_k Estimate the optimal number of cluster 'k' for a scRNA-Seq expression matrix
sc3_estimate_k-method Estimate the optimal number of cluster 'k' for a scRNA-Seq expression matrix
sc3_estimate_k.SingleCellExperiment Estimate the optimal number of cluster 'k' for a scRNA-Seq expression matrix
sc3_export_results_xls Write 'SC3' results to Excel file
sc3_export_results_xls-method Write 'SC3' results to Excel file
sc3_export_results_xls.SingleCellExperiment Write 'SC3' results to Excel file
sc3_interactive Opens 'SC3' results in an interactive session in a web browser.
sc3_interactive, Opens 'SC3' results in an interactive session in a web browser.
sc3_interactive-method Opens 'SC3' results in an interactive session in a web browser.
sc3_interactive.SingleCellExperiment Opens 'SC3' results in an interactive session in a web browser.
sc3_kmeans 'kmeans' clustering of cells.
sc3_kmeans, 'kmeans' clustering of cells.
sc3_kmeans-method 'kmeans' clustering of cells.
sc3_kmeans.SingleCellExperiment 'kmeans' clustering of cells.
sc3_plot_cluster_stability Plot stability of the clusters
sc3_plot_cluster_stability, Plot stability of the clusters
sc3_plot_cluster_stability-method Plot stability of the clusters
sc3_plot_cluster_stability.SingleCellExperiment Plot stability of the clusters
sc3_plot_consensus Plot consensus matrix as a heatmap
sc3_plot_consensus, Plot consensus matrix as a heatmap
sc3_plot_consensus-method Plot consensus matrix as a heatmap
sc3_plot_consensus.SingleCellExperiment Plot consensus matrix as a heatmap
sc3_plot_de_genes Plot expression of DE genes of the clusters identified by 'SC3' as a heatmap
sc3_plot_de_genes, Plot expression of DE genes of the clusters identified by 'SC3' as a heatmap
sc3_plot_de_genes-method Plot expression of DE genes of the clusters identified by 'SC3' as a heatmap
sc3_plot_de_genes.SingleCellExperiment Plot expression of DE genes of the clusters identified by 'SC3' as a heatmap
sc3_plot_expression Plot expression matrix used for SC3 clustering as a heatmap
sc3_plot_expression, Plot expression matrix used for SC3 clustering as a heatmap
sc3_plot_expression-method Plot expression matrix used for SC3 clustering as a heatmap
sc3_plot_expression.SingleCellExperiment Plot expression matrix used for SC3 clustering as a heatmap
sc3_plot_markers Plot expression of marker genes identified by 'SC3' as a heatmap.
sc3_plot_markers, Plot expression of marker genes identified by 'SC3' as a heatmap.
sc3_plot_markers-method Plot expression of marker genes identified by 'SC3' as a heatmap.
sc3_plot_markers.SingleCellExperiment Plot expression of marker genes identified by 'SC3' as a heatmap.
sc3_plot_silhouette Plot silhouette indexes of the cells
sc3_plot_silhouette, Plot silhouette indexes of the cells
sc3_plot_silhouette-method Plot silhouette indexes of the cells
sc3_plot_silhouette.SingleCellExperiment Plot silhouette indexes of the cells
sc3_prepare Prepare the 'SingleCellExperiment' object for 'SC3' clustering.
sc3_prepare-method Prepare the 'SingleCellExperiment' object for 'SC3' clustering.
sc3_prepare.SingleCellExperiment Prepare the 'SingleCellExperiment' object for 'SC3' clustering.
sc3_run_svm Run the hybrid 'SVM' approach.
sc3_run_svm, Run the hybrid 'SVM' approach.
sc3_run_svm-method Run the hybrid 'SVM' approach.
sc3_run_svm.SingleCellExperiment Run the hybrid 'SVM' approach.
support_vector_machines Run support vector machines ('SVM') prediction
tmult Matrix left-multiplied by its transpose
transformation Distance matrix transformation
yan Single cell RNA-Seq data extracted from a publication by Yan et al.